Human topoisomerase type I (Top1) is a ubiquitous cellular enzyme. It is a member of the topoisomerase family of enzymes that solve DNA topological problems associated with supercoiling. DNA supercoiling occurs during a number of vital cellular processes such as replication, transcription, and DNA repair. Top1 relaxes DNA by producing reversible single-strand DNA cuts. The generally accepted mechanism of Top1 action involves formation of a covalent link between the catalytic tyrosine 723 residue of Top1 and the 3′-end of the cut DNA strand in the Top1-DNA cleavage complex (Top1-DNAcc). The rotation of the 5′-end around the intact strand allows for relaxation of the supercoils. Once the tension caused by supercoiling has been removed, the backbone of the cut strand is religated and Top1 released. This mechanism has been substantiated by crystallography of a stable form of the Top1-DNAcc.
The dependency of living organisms on topoisomerases in processes like DNA replication during cell division has made topoisomerases attractive drug targets for anticancer chemotherapy. The search for Top1 inhibitors was eventually rewarded with the isolation of camptothecin (1) in 1966 from an extract of the Chinese tree Camptotheca acuminata.

It was found that camptothecin was capable of inducing DNA cleavage in the presence of Top1. The ability of camptothecin to bind to and stabilize the Top1-DNAcc by forming a drug-Top1-DNA ternary complex lies at the heart of its mechanism of action. Further development of camptothecin as an anticancer drug was hindered by its poor water solubility. Screening of a number of synthetic analogues of camptothecin led to the clinically used Top1 inhibitors, topotecan and irinotecan, which possess basic functionality and thus improved water solubility and bioavailability. Unfortunately, the derivatives of camptothecin have limitations in their clinical use. The lactone form is in equilibrium with its carboxylate form at physiological pH, which has reduced bioavailability due to plasma protein binding. Additionally, the treatment with derivatives of camptothecin requires long infusion times due to quick reversibility of the Top1-DNAcc.
Crystallography of the camptothecin-Top1-DNA ternary complex revealed that camptothecin is capable of stabilizing the Top1-DNAcc by binding to it at the site of cleavage.
The described binding mode showed an extended region of π-π stacking between the polycyclic core of camptothecin and the DNA base pairs, as well as a number of polar interactions formed between camptothecin and Top1 residues. The intercalation of camptothecin into the Top1-DNAcc increases the distance between ends of the broken DNA strand and prevents religation, resulting in prolonged covalent attachment of Top1 to the DNA.
A new class of Top1 inhibitors, the indenoisoquinolines, emerged with the isolation of NSC 314622 (2) as a byproduct of nitidine chloride synthesis.

A COMPARE analysis revealed similar cytotoxicity profiles between (1) and (2). However, observed differences in DNA cleavage site specificity between camptothecins and indenoisoquinolines suggested that different genes might be targeted more specifically with indenoisoquinolines. Also and in contrast to (1), the Top1-DNAcc trapped by (2) was more persistent in both cell- and enzyme-based assays. Moreover, a structural comparison of the indenoisoquinolines and the camptothecins suggested that indenoisoquinolines would likely have enhanced chemical stability relative to that of the camptothecins. Further structure optimization of (2) and biological assessment of synthesized analogues led to the discovery of a number of potent Top1 inhibitors, including MJIII-65 (3a), NSC 724998 (NSC 743400, LMP400, 3b), and NSC725776 (LMP776, 3c). The morpholinopropyl (3b) and imidazolylpropyl (3c) compounds have been promoted to phase I clinical trials at National Cancer Institute.

It has been discovered that azaindenoisoquinolines, as described below, demonstrate improved water solubility without any decrease in Top1 inhibitory activity or cytotoxicity. Analysis of the biological results reveals that smaller lactam ring substituents enable intercalation into both free DNA and Top1-DNA cleavage complex, whereas larger substituents only allow binding to the cleavage complex but not free DNA. Free DNA binding suppresses Top1-catalyzed DNA cleavage at high drug concentrations, whereas DNA cleavage and inhibition of religation occurs at low drug concentration.
In one illustrative embodiment of the invention, a compound of the following formula:
or a pharmaceutically acceptable salt thereof, wherein each of W, X, Y, Z, RA, RB, RC, RD and RE is defined below, is described herein.
In addition, various genera and subgenera of each of W, X, Y, Z, RA, RB, RC, RD and RE are described herein. It is to be understood that all possible combinations of the various genera and subgenera of each of W, X, Y, Z, RA, RB, RC, RD and RE described herein represent additional illustrative embodiments of compounds of the invention described herein. It is to be further understood that each of those additional illustrative embodiments of compounds may be used in any of the compositions, methods, and/or uses described herein.
In another embodiment, pharmaceutical compositions containing one or more of the compounds are also described herein. In one aspect, the compositions include a therapeutically effective amount of the one or more compounds for treating a patient with cancer. It is to be understood that the compositions may include other component and/or ingredients, including, but not limited to, other therapeutically active compounds, and/or one or more carriers, diluents, excipients, and the like. In another embodiment, methods for using the compounds and pharmaceutical compositions for treating patients with cancer are also described herein. In one aspect, the methods include the step of administering one or more of the compounds and/or compositions described herein to a patient with cancer. In another aspect, the methods include administering a therapeutically effective amount of the one or more compounds and/or compositions described herein for treating patients with cancer.
It is appreciated herein that the compounds described herein may be used alone or in combination with other compounds useful for treating cancer, including those compounds that may be therapeutically effective by the same or different modes of action. In addition, it is appreciated herein that the compounds described herein may be used in combination with other compounds that are administered to treat other symptoms of cancer, such as compounds administered to relieve nausea, vomiting, pain, and the like.